User guide

This guide provides

• material introducing GROMACS
• practical advice for making effective use of GROMACS.

For getting, building and installing GROMACS, see the Installation guide. For background on algorithms and implementations, see the reference manual.

• Getting started
  • Setting up your environment
  • Flowchart of typical simulation
  • Important files
  • Tutorial material
  • Background reading
• System preparation
  • Steps to consider
  • Tips and tricks
• Managing long simulations
  • Appending to output files
  • Backing up your files
  • Extending a .tpr file
  • Changing mdp options for a restart
  • Restarts without checkpoint files
  • Are continuations exact?
  • Reproducibility
• Answers to frequently asked questions (FAQs)
  • Questions regarding GROMACS installation
  • Questions concerning system preparation and preprocessing
  • Questions regarding simulation methodology
  • Parameterization and Force Fields
  • Analysis and Visualization
• Force fields in GROMACS
  • AMBER
  • CHARMM
  • GROMOS
  • OPLS
• Non-bonded cut-off schemes
  • Non-bonded scheme feature comparison
  • Performance
  • How to use the Verlet scheme
  • Further information
• Command-line reference
  • Command-line interface and conventions
  • Commands by name
  • Commands by topic
  • Special topics
  • Command changes between versions
• Molecular dynamics parameters (.mdp options)
  • General information
• Useful mdrun features
  • Re-running a simulation
  • Running a simulation in reproducible mode
  • Running multi-simulations
  • Controlling the length of the simulation
  • Running a membrane protein embedding simulation
• Getting good performance from mdrun
  • Hardware background information
  • GROMACS background information
  • Running mdrun within a single node
  • Running mdrun on more than one node
  • Controlling the domain decomposition algorithm
  • Finding out how to run mdrun better
  • Running mdrun with GPUs
  • Running the OpenCL version of mdrun
  • Performance checklist
• Common errors when using GROMACS
  • Common errors during usage
  • Errors in pdb2gmx
  • Errors in grompp
  • Errors in mdrun
• File formats
  • Summary of file formats
  • File format details
• Terminology
  • Pressure
  • Periodic boundary conditions
  • Thermostats
  • Energy conservation
  • Average structure
  • Blowing up
  • Diagnosing an unstable system
  • Molecular dynamics
  • Force field
• Environment Variables
  • Output Control
  • Debugging
  • Performance and Run Control
  • OpenCL management
  • Analysis and Core Functions
• Floating point arithmetic
• Security when using GROMACS